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Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis

, Sara C. Madeira, , Mamede de Carvalho, Alexandra M. Carvalho
Published: 1 May 2021
Journal of Biomedical Informatics , Volume 117; doi:10.1016/j.jbi.2021.103730

Abstract: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease causing patients to quickly lose motor neurons. The disease is characterized by a fast functional impairment and ventilatory decline, leading most patients to die from respiratory failure. To estimate when patients should get ventilatory support, it is helpful to adequately profile the disease progression. For this purpose, we use dynamic Bayesian networks (DBNs), a machine learning model, that graphically represents the conditional dependencies among variables. However, the standard DBN framework only includes dynamic (time-dependent) variables, while most ALS datasets have dynamic and static (time-independent) observations. Therefore, we propose the sdtDBN framework, which learns optimal DBNs with static and dynamic variables. Besides learning DBNs from data, with polynomial-time complexity in the number of variables, the proposed framework enables the user to insert prior knowledge and to make inference in the learned DBNs. We use sdtDBNs to study the progression of 1214 patients from a Portuguese ALS dataset. First, we predict the values of every functional indicator in the patients’ consultations, achieving results competitive with state-of-the-art studies. Then, we determine the influence of each variable in patients’ decline before and after getting ventilatory support. This insightful information can lead clinicians to pay particular attention to specific variables when evaluating the patients, thus improving prognosis. The case study with ALS shows that sdtDBNs are a promising predictive and descriptive tool, which can also be applied to assess the progression of other diseases, given time-dependent and time-independent clinical observations.
Keywords: Amyotrophic lateral sclerosis / Probabilistic graphical models / Dynamic Bayesian networks / Polynomial-time optimal algorithm / Disease progression / Time variant and time invariant variables

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